Objective To compare the clinical effect between high flow rate modified ultrafiltration （HMUF） and conventional modified ultrafiltration（CMUF）, and the effect on hemodynamic data and inflammatory mediators. Methods Forty children were divided into two groups with random number table, HMUF group and CMUF group, 20 cases each group. Hematocrit （HCT） and hemodynamic changes were recorded and the concentration of tumor necrosis factor （TNF） and interleukin 6 （IL-6） were measured. Results The operations were done uneventfully with moderate hypothermia cardiopulmonary bypass in 40 patients. Duration of ultrafiltration of HMUF group （7.83±0. 75 min） was less than that of CMUF group （13.86±1.95 min, P〈0.01）. The volumes ultrafiltrated of HMUF group （440.00±91.86ml） was more than that of CMUF group （372.22±56.52ml, P〈0.01）. There are no significant differences about the hemodynamic data, HCT, TNF and IL-6 between two groups. Conclusion The HMUF is safe and efficient,when it was used after pediatric cardiopulmonary bypass, the duration of ultrafiltration can be shortened significantly.